Index Catalog // ScholarsArchive@OSU

High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding

Creator:: Sim, Sung-Chur, Van Deynze, Allen, Stoffel, Kevin, Douches, David S., Zarka, Daniel, Ganal, Martin W., Chetelat, Roger T., Hutton, Samuel F., Scott, John W., Gardner, Randolph G., Panthee, Dilip R., Mutschler, Martha, Myers, James R., and Francis, David M.
Abstract:: The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal...
Resource Type:: Article
Full Text:: TraitGenetics GmbH, Gatersleben, Germany, 5 C. M. Rick Tomato Genetic Resource Center, University of California

Closing a gap in tropical forest biomass estimation: taking crown mass variation into account in pantropical allometries

Creator:: Ploton, Pierre, Barbier, Nicolas, Takoudjou Momo, Stéphane, Réjou-Méchain, Maxime, Boyemba Bosela, Faustin, Chuyong, Georges, Dauby, Gilles, Droissart, Vincent, Fayolle, Adeline, Goodman, Rosa Calisto, Henry, Matieu, Kamdem, Narcisse Guy, Mukirania, John Katembo, Kenfack, David, Libalah, Moses, Ngomanda, Alfred, Rossi, Vivien, Sonké, Bonaventure, Texier, Nicolas, Thomas, Duncan, Zebaze, Donatien, Couteron, Pierre, Berger, Uta, and Pélissier, Raphaël
Abstract:: Accurately monitoring tropical forest carbon stocks is a challenge that remains outstanding. Allometric models that consider tree diameter, height and wood density as predictors are currently used in most tropical forest carbon studies. In particular, a pantropical biomass model has been widely used for approximately a decade, and its most...
Resource Type:: Article

Gas transport in firn: multiple-tracer characterisation and model intercomparison for NEEM, Northern Greenland

Creator:: Buizert, C., Martinerie, P., Petrenko, V. V., Severinghaus, J. P., Trudinger, C. M., Witrant, E., Rosen, J. L., Orsi, A. J., Rubino, M., Etheridge, D. M., Steele, L. P., Hogan, C., Laube, J. C., Sturges, W. T., Levchenko, V. A., Smith, A. M., Levin, I., Conway, T. J., Dlugokencky, E. J., Lang, P. M., Kawamura, K., Jenk, T. M., White, J. W. C., Sowers, T., Schwander, J., and Blunier, T.
Abstract:: Air was sampled from the porous firn layer at the NEEM site in Northern Greenland. We use an ensemble of ten reference tracers of known atmospheric history to characterise the transport properties of the site. By analysing uncertainties in both data and the reference gas atmospheric histories, we can objectively...
Resource Type:: Article

WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks

Creator:: Hanumappa, Mamatha, Preece, Justin, Elser, Justin, Nemeth, Denise, Bono, Gina, Wu, Kenny, and Jaiswal, Pankaj
Abstract:: Background: Next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. Despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated...
Resource Type:: Article
Full Text:: (PGS) application in saving valuable time and labor when a reference network in one species compiled in

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

Creator:: Dharmawardhana, Palitha, Ren, Liya, Amarasinghe, Vindhya, Monaco, Marcela, Thomason, Jim, Ravenscroft, Dean, McCouch, Susan, Ware, Doreen, and Jaiswal, Pankaj
Abstract:: Background: Functional annotations of large plant genome projects mostly provide information on gene function and gene families based on the presence of protein domains and gene homology, but not necessarily in association with gene expression or metabolic and regulatory networks. These additional annotations are necessary to understand the physiology, development...
Resource Type:: Article
Full Text:: predicted based on MetaCyc reference networks and plant pathways from the Plant Metabolic Network, using the

A Multi-Year Longitudinal Study of Water Quality Parameters in Four Salmon-Bearing and Recreational Streams on Mount Hood, Oregon

Creator:: Wasowski, Ronald, Alexander, David, Kolmes, Steven, Banet, Nathan, Card, Amy, Haines, Morgan, Kolmes, Elijah, Northcutt, Kelly, Roemer, Derek, and Webber, Sarah
Abstract:: Four streams-Clear Fork, Lost Creek, Camp Creek and Still Creek-in northwestern Oregon's Sandy River Basin were monitored for temperature, dissolved oxygen levels, and fecal bacterial concentrations in a multi-year analysis examining stream health for recreational users and anchor habitat for Pacific Salmon. Temperatures were recorded using micro -T temperature loggers...
Resource Type:: Article
Full Text:: Department of Fish and Wildlife, Salem, Oregon, United States of America, 5 Mathey College, Princeton

CoastColour Round Robin data sets: a database to evaluate the performance of algorithms for the retrieval of water quality parameters in coastal waters

Creator:: Nechad, B., Ruddick, K., Schroeder, T., Oubelkheir, K., Blondeau-Patissier, D., Cherukuru, N., Brando, V., Dekker, A., Clementson, L., Banks, A. C., Maritorena, S., Werdell, P. J., Sá, C., Brotas, V., Caballero de Frutos, I., Ahn, Y., Salama, S., Tilstone, G., Martinez-Vicente, V., Foley, D., McKibben, M., Nahorniak, J., Peterson, T., Siliò-Calzada, A., Röttgers, R., Lee, Z., Peters, M., and Brockmann, C.
Abstract:: The use of in situ measurements is essential in the validation and evaluation of the algorithms that provide coastal water quality data products from ocean colour satellite remote sensing. Over the past decade, various types of ocean colour algorithms have been developed to deal with the optical complexity of coastal...
Resource Type:: Article

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

Creator:: Bushley, Kathryn E., Raja, Rajani, Jaiswal, Pankaj, Cumbie, Jason S., Nonogaki, Mariko, Boyd, Alexander E., Owensby, C. Alisha, Knaus, Brian J., Elser, Justin, Miller, Daniel, Di, Yanming, McPhail, Kerry L., and Spatafora, Joseph W.
Abstract:: The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of...
Resource Type:: Article
Full Text:: reference draft genome of Ophiocordycipitaceae, a third family of insect pathogenic fungi within the fungal

The WAIS Divide deep ice core WD2014 chronology - Part 2: Annual-layer counting (0-31 ka BP)

Creator:: Sigl, Michael, Fudge, Tyler J., Winstrup, Mai, Cole-Dai, Jihong, Ferris, David, McConnell, Joseph R., Taylor, Ken C., Welten, Kees C., Woodruff, Thomas E., Adolphi, Florian, Bisiaux, Marion, Brook, Edward J., Buizert, Christo, Caffee, Marc W., Dunbar, Nelia W., Edwards, Ross, Geng, Lei, Iverson, Nels, Koffman, Bess, Layman, Lawrence, Maselli, Olivia J., McGwire, Kenneth, Muscheler, Raimund, Nishiizumi, Kunihiko, Pasteris, Daniel R., Rhodes, Rachael H., and Sowers, Todd A
Abstract:: We present the WD2014 chronology for the upper part (0–2850 m; 31.2 ka BP) of the West Antarctic Ice Sheet (WAIS) Divide (WD) ice core. The chronology is based on counting of annual layers observed in the chemical, dust and electrical conductivity records. These layers are caused by seasonal changes...
Resource Type:: Article

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

Creator:: Bruskiewich, Richard, Senger, Martin, Davenport, Guy, Ruiz, Manuel, Rouard, Mathieu, Hazekamp, Tom, Takeya, Masaru, Doi, Koji, Satoh, Kouji, Costa, Marcos, Simon, Reinhard, Balaji, Jayashree, Akintunde, Akinnola, Mauleon, Ramil, Wanchana, Samart, Shah, Trushar, Anacleto, Mylah, Portugal, Arllet, Ulat, Victor Jun, Thongjuea, Supat, Braak, Kyle, Ritter, Sebastian, Dereeper, Alexis, Skofic, Milko, Rojas, Edwin, Martins, Natalia, Pappas, Georgios, Alamban, Ryan, Almodiel, Roque, Barboza, Lord Hendrix, Detras, Jeffrey, Manansala, Kevin, Mendoza, Michael Jonathan, Morales, Jeffrey, Peralta, Barry, Valerio, Rowena, Zhang, Yi, Gregorio, Sergio, Hermocilla, Joseph, Echavez, Michael, Yap, Jan Michael, Farmer, Andrew, Schiltz, Gary, Lee, Jennifer, Casstevens, Terry, Jaiswal, Pankaj, Meintjes, Ayton, Wilkinson, Mark, Good, Benjamin, Wagner, James, Morris, Jane, Marshall, David, Collins, Anthony, Kikuchi, Shoshi, Metz, Thomas, McLaren, Graham, and van Hintum, Theo
Abstract:: The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the...
Resource Type:: Article
Full Text:: Guy Davenport,2 Manuel Ruiz,3 Mathieu Rouard,4 TomHazekamp,4 Masaru Takeya,5 Koji Doi,5 Kouji Satoh,5

ScholarsArchive@OSU

High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding

Closing a gap in tropical forest biomass estimation: taking crown mass variation into account in pantropical allometries

Gas transport in firn: multiple-tracer characterisation and model intercomparison for NEEM, Northern Greenland

WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

A Multi-Year Longitudinal Study of Water Quality Parameters in Four Salmon-Bearing and Recreational Streams on Mount Hood, Oregon

CoastColour Round Robin data sets: a database to evaluate the performance of algorithms for the retrieval of water quality parameters in coastal waters

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

The WAIS Divide deep ice core WD2014 chronology - Part 2: Annual-layer counting (0-31 ka BP)

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

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